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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ), 'gf_id' => 'HOM05D001361', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001361' ), 'data_identifier' => 'HOM05D001361', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001361', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p43520' => 'bna', 'A07p13190' => 'bna', 'A08p26450' => 'bna', 'A08p27700' => 'bna', 'A09p23940' => 'bna', 'A09p38670' => 'bna', 'A09p38680' => 'bna', 'A09p40430' => 'bna', 'A10p03390' => 'bna', 'Aa31LG1G20040' => 'aar', 'Aa31LG2G7530' => 'aar', 'Aa31LG7G8150' => 'aar', 'Aa31LG7G9930' => 'aar', 'Aa31LG7G9940' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2868' => 'aag', 'Actinidia03190' => 'ach', 'Actinidia08055' => 'ach', 'Actinidia08057' => 'ach', 'Actinidia08216' => 'ach', 'Actinidia30631' => 'ach', 'Actinidia34024' => 'ach', 'Actinidia39801' => 'ach', 'Ah.02g130800' => 'amhyb', 'AL1G14690' => 'aly', 'AL1G38520' => 'aly', 'AL1G40660' => 'aly', 'AL1G40670' => 'aly', 'AL5G11920' => 'aly', 'Aqoxy1G02844' => 'aox', 'Aqoxy261s001' => 'aox', 'Aqoxy3G00747' => 'aox', 'Aqoxy3G03283' => 'aox', 'Aqoxy5G03301' => 'aox', 'Aqoxy93s001' => 'aox', 'Aqoxy93s002' => 'aox', 'arahy.Tifrunner.gnm1.ann1.KTR52G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M8JYJC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M9HGBQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZWE21' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PUF87X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S44JZV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WMQ7N5' => 'arhy', 'AT1G04960' => 'ath', 'AT1G24265' => 'ath', 'AT1G24267' => 'ath', 'AT1G27000' => 'ath', 'AT2G02730' => 'ath', 'ATR0561G106' => 'atr', 'ATR1101G011' => 'atr', 'ATR1120G156' => 'atr', 'Atru.chr11.1898' => 'acertr', 'Atru.chr11.2355' => 'acertr', 'Atru.chr6.1371' => 'acertr', 'Atru.chr6.3283' => 'acertr', 'Atru.chr6.3286' => 'acertr', 'Atru.chr6.3300' => 'acertr', 'AUR62005647' => 'cqu', 'AUR62005733' => 'cqu', 'AUR62015102' => 'cqu', 'AUR62017563' => 'cqu', 'AUR62028828' => 'cqu', 'AUR62028903' => 'cqu', 'BcaB03g12068' => 'bca', 'BcaB03g12069' => 'bca', 'BcaB07g30695' => 'bca', 'BcaB08g34741' => 'bca', 'BcaC01g01627' => 'bca', 'BcaC04g21517' => 'bca', 'BcaC05g26354' => 'bca', 'BcaC05g26539' => 'bca', 'BcaC05g26540' => 'bca', 'BcaC05g26733' => 'bca', 'BcaC05g26734' => 'bca', 'BcaC06g31220' => 'bca', 'BcaC06g34044' => 'bca', 'BolC3t19653H' => 'bol', 'BolC5t29093H' => 'bol', 'BolC5t31098H' => 'bol', 'BolC5t31314H' => 'bol', 'BolC5t31315H' => 'bol', 'BolC7t43844H' => 'bol', 'BolC8t49899H' => 'bol', 'BolC9t55945H' => 'bol', 'BraA06t27237Z' => 'bra', 'BraA08t34597Z' => 'bra', 'BraA08t34705Z' => 'bra', 'BraA09t39375Z' => 'bra', 'BraA09t39376Z' => 'bra', 'BraA09t39539Z' => 'bra', 'BraA10t42615Z' => 'bra', 'C03p73600' => 'bna', 'C05p03110' => 'bna', 'C05p23790' => 'bna', 'C05p25950' => 'bna', 'C05p25960' => 'bna', 'C07p33340' => 'bna', 'C08p22610' => 'bna', 'C09p30830' => 'bna', 'CAN.G1358.16' => 'can', 'CAN.G137.6' => 'can', 'CAN.G416.38' => 'can', 'CAN.G567.33' => 'can', 'CAN.G726.10' => 'can', 'CANSAT01G0548' => 'cansat', 'CANSAT64G0039' => 'cansat', 'CANSAT64G0710' => 'cansat', 'CARHR004370' => 'chi', 'CARHR024910' => 'chi', 'CARHR026830' => 'chi', 'CARHR026840' => 'chi', 'CARHR145160' => 'chi', 'Carub.0001s0420' => 'cru', 'Carub.0001s2397' => 'cru', 'Carub.0001s2579' => 'cru', 'Carub.0001s2580' => 'cru', 'Carub.0005s0164' => 'cru', 'Ca_04747_v3' => 'car', 'Ca_07127_v3' => 'car', 'Ca_16351_v3' => 'car', 'CBR_g31155' => 'cbr', 'Cc11_g17160' => 'ccan', 'CDE02G3199' => 'cde', 'CDE02G3302' => 'cde', 'CDE05G0317' => 'cde', 'CDE05G1789' => 'cde', 'CDE06G0592' => 'cde', 'CDE09G0127' => 'cde', 'Cfa009024' => 'cfa', 'Cfa009384' => 'cfa', 'Ciclev10018308m.g' => 'ccl', 'Ciclev10031908m.g' => 'ccl', 'Ciclev10033518m.g' => 'ccl', 'CiPaw.03G274500' => 'cil', 'CiPaw.05G107400' => 'cil', 'CiPaw.05G139100' => 'cil', 'CiPaw.06G081200' => 'cil', 'ClCG01G018850' => 'cla', 'ClCG02G009670' => 'cla', 'ClCG06G002090' => 'cla', 'COL.COLO4_05389' => 'col', 'COL.COLO4_20443' => 'col', 'COL.COLO4_23041' => 'col', 'Cpa.g.c28586.2' => 'cpa', 'Cpa.g.sc132.53' => 'cpa', 'Cpa.g.sc200.23' => 'cpa', 'Cpa.g.sc43.83' => 'cpa', 'Cpa.g.sc43.84' => 'cpa', 'Cre16.g668350' => 'cre', 'CsaV3_2G034350' => 'csa', 'CsaV3_6G008160' => 'csa', 'CsaV3_6G045510' => 'csa', 'CSS0002134' => 'camsi', 'CSS0006201' => 'camsi', 'CSS0018559' => 'camsi', 'CSS0020990' => 'camsi', 'CSS0023699' => 'camsi', 'CSS0025195' => 'camsi', 'CSS0035859' => 'camsi', 'CSS0038700' => 'camsi', 'CSS0039250' => 'camsi', 'CSS0040349' => 'camsi', 'CSS0043997' => 'camsi', 'CSS0045607' => 'camsi', 'CSS0049047' => 'camsi', 'DCAR_004275' => 'dca', 'DCAR_019734' => 'dca', 'DCAR_024667' => 'dca', 'DCAR_028265' => 'dca', 'DCAR_028266' => 'dca', 'Dinv08702' => 'din', 'Dinv17585' => 'din', 'Dinv43649' => 'din', 'Dinv44088' => 'din', 'Duzib138G1844' => 'dzi', 'Duzib248G0082' => 'dzi', 'Duzib248G0766' => 'dzi', 'Duzib251G0004' => 'dzi', 'Duzib251G0880' => 'dzi', 'Duzib268G1250' => 'dzi', 'ECA234G3613' => 'eca', 'ECA240G0476' => 'eca', 'ECA246G4360' => 'eca', 'ECA246G4804' => 'eca', 'EL10Ac6g13158' => 'bvu', 'EL10Ac6g13534' => 'bvu', 'EL10Ac6g15295' => 'bvu', 'EL10Ac9g22785' => 'bvu', 'Eucgr.A01083' => 'egr', 'Eucgr.B03413' => 'egr', 'Eucgr.B03519' => 'egr', 'FAN02G3926' => 'fan', 'FAN05G2080' => 'fan', 'FAN07G0196' => 'fan', 'FAN07G1559' => 'fan', 'FAN09G0446' => 'fan', 'FAN12G2218' => 'fan', 'FAN14G2423' => 'fan', 'FAN17G0717' => 'fan', 'FAN17G1883' => 'fan', 'FAN22G1943' => 'fan', 'FvH4_1g20311' => 'fve', 'FvH4_4g23490' => 'fve', 'FvH4_4g31870' => 'fve', 'FvH4_6g41750' => 'fve', 'Glyma.01G042800' => 'gma', 'Glyma.02G020800' => 'gma', 'Glyma.08G259700' => 'gma', 'Glyma.18G283800' => 'gma', 'Gohir.A03G124400' => 'ghi', 'Gohir.A04G141200' => 'ghi', 'Gohir.A11G151600' => 'ghi', 'Gohir.A12G166300' => 'ghi', 'Gohir.A13G072100' => 'ghi', 'Gohir.D02G057300' => 'ghi', 'Gohir.D02G146800' => 'ghi', 'Gohir.D04G022372' => 'ghi', 'Gohir.D04G027950' => 'ghi', 'Gohir.D04G084248' => 'ghi', 'Gohir.D04G187700' => 'ghi', 'Gohir.D05G291300' => 'ghi', 'Gohir.D08G096500' => 'ghi', 'Gohir.D09G047000' => 'ghi', 'Gohir.D10G160200' => 'ghi', 'Gohir.D11G158600' => 'ghi', 'Gohir.D11G231540' => 'ghi', 'Gohir.D12G169800' => 'ghi', 'Gohir.D13G067800' => 'ghi', 'Gorai.005G164400' => 'gra', 'Gorai.006G051200' => 'gra', 'Gorai.007G169000' => 'gra', 'Gorai.008G182400' => 'gra', 'Gorai.012G030700' => 'gra', 'Gorai.012G180700' => 'gra', 'Gorai.013G077300' => 'gra', 'GSVIVG01010524001' => 'vvi', 'GSVIVG01019002001' => 'vvi', 'GSVIVG01020065001' => 'vvi', 'GSVIVG01030540001' => 'vvi', 'HanXRQChr05g0128771' => 'han', 'HanXRQChr06g0174761' => 'han', 'HanXRQChr12g0361331' => 'han', 'HanXRQChr13g0396491' => 'han', 'HanXRQChr14g0429251' => 'han', 'HanXRQChr17g0538121' => 'han', 'Haze_12055' => 'cav', 'Haze_12741' => 'cav', 'Hma1.2p1_0065F.1_g035150' => 'hma', 'Hma1.2p1_0133F.1_g060860' => 'hma', 'Hma1.2p1_0341F.1_g130600' => 'hma', 'HPP92_008062' => 'vpl', 'HPP92_008065' => 'vpl', 'HPP92_021790' => 'vpl', 'Hund02280' => 'sun', 'Hund25266' => 'sun', 'Hund25479' => 'sun', 'Lalb_Chr04g0256311' => 'lal', 'Lalb_Chr10g0092051' => 'lal', 'Lalb_Chr14g0362551' => 'lal', 'Lalb_Chr17g0336401' => 'lal', 'Lj1C785T7' => 'lonja', 'Lj2g0009692' => 'lja', 'Lj2g0024699' => 'lja', 'Lj3C1072T8' => 'lonja', 'Lj5g0005237' => 'lja', 'Lj6A829G28' => 'lonja', 'Lsat_1_v5_gn_3_19241' => 'lsa', 'Lsat_1_v5_gn_3_31340' => 'lsa', 'Lsat_1_v5_gn_4_34480' => 'lsa', 'Lsat_1_v5_gn_6_3540' => 'lsa', 'Lsat_1_v5_gn_9_105360' => 'lsa', 'Manes.01G189500' => 'mes', 'Manes.05G097501' => 'mes', 'Manes.12G008800' => 'mes', 'Manes.12G056000' => 'mes', 'Manes.13G009200' => 'mes', 'Mapoly0031s0188' => 'mpo', 'MBI04_g10405_MAGBIO' => 'mbi', 'MBI07_g21496_MAGBIO' => 'mbi', 'MBI11_g05341_MAGBIO' => 'mbi', 'MBI16_g07774_MAGBIO' => 'mbi', 'MBI16_g41623_MAGBIO' => 'mbi', 'MD05G1007200' => 'mdo', 'MD09G1117500' => 'mdo', 'MD13G1078200' => 'mdo', 'MD13G1122000' => 'mdo', 'MD16G1077900' => 'mdo', 'MD16G1122300' => 'mdo', 'MD17G1108700' => 'mdo', 'Medtr3g082850' => 'mtr', 'Medtr5g038550' => 'mtr', 'Medtr7g022230' => 'mtr', 'MELO3C007764.2' => 'cme', 'MELO3C019349.2' => 'cme', 'MELO3C022320.2' => 'cme', 'Migut.A01170' => 'egut', 'Migut.E00542' => 'egut', 'Migut.E00752' => 'egut', 'Migut.K00986' => 'egut', 'MSTRG.12169' => 'ama', 'MSTRG.24843' => 'ama', 'MSTRG.486' => 'ama', 'MSTRG.8019' => 'ama', 'Nitab4.5_0000411g0030' => 'nta', 'Nitab4.5_0000411g0040' => 'nta', 'Nitab4.5_0000556g0200' => 'nta', 'Nitab4.5_0000834g0010' => 'nta', 'Nitab4.5_0002367g0070' => 'nta', 'Nitab4.5_0002778g0040' => 'nta', 'Nitab4.5_0002793g0060' => 'nta', 'Nitab4.5_0008235g0020' => 'nta', 'Nitab4.5_0010664g0010' => 'nta', 'Nn1g07359' => 'nnu', 'Nn3g16410' => 'nnu', 'Nn4g22268' => 'nnu', 'Nn4g23060' => 'nnu', 'Oeu000753.1' => 'oeu', 'Oeu004465.2' => 'oeu', 'Oeu006513.1' => 'oeu', 'Oeu017067.2' => 'oeu', 'Oeu018601.1' => 'oeu', 'Oeu027077.1' => 'oeu', 'Os01g0100800' => 'osa', 'Os01g0112300' => 'osa', 'Os01g0185100' => 'osa', 'Os05g0103700' => 'osa', 'Os05g0182700' => 'osa', 'Os09g0482740' => 'osa', 'Peaxi162Scf00023g02226' => 'pax', 'Peaxi162Scf00045g00217' => 'pax', 'Peaxi162Scf00074g00056' => 'pax', 'Peaxi162Scf00128g01540' => 'pax', 'Peaxi162Scf00456g00212' => 'pax', 'PGR042G3486' => 'pgr', 'PGR102G1867' => 'pgr', 'PGR102G2437' => 'pgr', 'PGR119G1577' => 'pgr', 'PGSC0003DMG400012257' => 'stu', 'PGSC0003DMG400015124' => 'stu', 'PGSC0003DMG400015148' => 'stu', 'PGSC0003DMG400023309' => 'stu', 'Phvul.002G065900' => 'pvu', 'Phvul.008G017700' => 'pvu', 'Phvul.L003137' => 'pvu', 'Potri.001G058700' => 'ptr', 'Potri.002G219300' => 'ptr', 'Potri.003G169200' => 'ptr', 'Potri.008G149000' => 'ptr', 'Potri.010G030400' => 'ptr', 'Potri.010G092700' => 'ptr', 'Potri.014G160800' => 'ptr', 'Pp3c10_5340' => 'ppa', 'Pp3c1_21100' => 'ppa', 'Pp3c25_15090' => 'ppa', 'Prupe.1G223300' => 'ppe', 'Prupe.1G268900' => 'ppe', 'Prupe.1G476000' => 'ppe', 'Prupe.2G092400' => 'ppe', 'Prupe.3G110800' => 'ppe', 'Prupe.3G206300' => 'ppe', 'Prupe.4G273100' => 'ppe', 'Psat2g144360' => 'psa', 'Psat3g188120' => 'psa', 'Psat5g103960' => 'psa', 'PSO017G4710' => 'pso', 'PSO478G4435' => 'pso', 'PSO478G4880' => 'pso', 'PSO541G2939' => 'pso', 'PSO591G0091' => 'pso', 'PSO675G6158' => 'pso', 'PSO782G4495' => 'pso', 'PSO832G1946' => 'pso', 'QL03p029156' => 'qlo', 'QL03p029172' => 'qlo', 'QL03p051832' => 'qlo', 'QL03p065510' => 'qlo', 'QL08p029756' => 'qlo', 'RcHm_v2.0_Chr2g0157541' => 'rch', 'RcHm_v2.0_Chr4g0429881' => 'rch', 'RcHm_v2.0_Chr4g0440531' => 'rch', 'Rhsim04G0046400' => 'rsi', 'Rhsim12G0024000' => 'rsi', 'Rhsim12G0057700' => 'rsi', 'Rhsim12G0130400' => 'rsi', 'Sabra01G0042200' => 'sbr', 'Sabra02G0170900' => 'sbr', 'Sabra02G0171000' => 'sbr', 'Sabra10G0050900' => 'sbr', 'Sabra14G0122500' => 'sbr', 'SalBow1G0997' => 'sbo', 'SalBow1G2500' => 'sbo', 'SalBow2G0873' => 'sbo', 'Sc04g0008420' => 'sci', 'Sc04g0010260' => 'sci', 'Sc05g0006270' => 'sci', 'Sed0011652' => 'sed', 'Sed0016155' => 'sed', 'Sed0022061' => 'sed', 'Sed0027422' => 'sed', 'SEGI_31967' => 'sgi', 'SGA_v2.0_scaffold114G31917' => 'sas', 'SGA_v2.0_scaffold198G41078' => 'sas', 'SGA_v2.0_scaffold258G45786' => 'sas', 'SGA_v2.0_scaffold54G19444' => 'sas', 'SGA_v2.0_scaffold65G22146' => 'sas', 'SGA_v2.0_scaffold7G04048' => 'sas', 'SMO334G0094' => 'smo', 'Solyc05g015820.4' => 'sly', 'Solyc08g005230.3' => 'sly', 'Solyc08g082730.4' => 'sly', 'Sopen05g011440' => 'spe', 'Sopen08g001260' => 'spe', 'Sopen08g030960' => 'spe', 'Sp1g03810' => 'spa', 'Sp1g21790' => 'spa', 'Sp1g23500' => 'spa', 'Sp1g23510' => 'spa', 'Sp2g13840' => 'spa', 'TAR371G0316' => 'tar', 'TAR371G0443' => 'tar', 'TAR629G0132' => 'tar', 'TAR629G2015' => 'tar', 'TAR629G2391' => 'tar', 'TAR629G2435' => 'tar', 'THA.LOC104801014' => 'tha', 'THA.LOC104807139' => 'tha', 'THA.LOC104822101' => 'tha', 'THA.LOC104822929' => 'tha', 'THA.LOC104825490' => 'tha', 'Thecc.01G187300' => 'tca', 'Thecc.02G202500' => 'tca', 'Thecc.02G354100' => 'tca', 'Thhalv10004758m.g' => 'esa', 'Thhalv10008045m.g' => 'esa', 'Thhalv10008078m.g' => 'esa', 'Thhalv10008218m.g' => 'esa', 'Thhalv10008298m.g' => 'esa', 'TPR.G18467' => 'tpr', 'TPR.G22467' => 'tpr', 'TPR.G2940' => 'tpr', 'TWI18G1247' => 'twi', 'TWI36G1404' => 'twi', 'TWI75G0070' => 'twi', 'TWI75G0976' => 'twi', 'unitig_22.g5611' => 'ugi', 'unitig_52.g17200' => 'ugi', 'unitig_699.g19796' => 'ugi', 'unitig_747.g21121' => 'ugi', 'vmacro01051' => 'vma', 'vmacro01232' => 'vma', 'vmacro09375' => 'vma', 'VMungo0540G1276' => 'vmu', 'VMungo1215G2637' => 'vmu', 'Zm00001eb121840' => 'zma', 'Zm00001eb282900' => 'zma', 'Zm00001eb285600' => 'zma', 'Zm00001eb316450' => 'zma', 'Zm00001eb334060' => 'zma', 'Zm00001eb346900' => 'zma', 'Zm00001eb356190' => 'zma' ) $gf_id = 'HOM05D001361' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001361' ) $data_identifier = 'HOM05D001361' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 19, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 3, 'ppe' => (int) 7, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 6, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356190' $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